[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

Dear Erik,

Thank you so much for the time and answer. Actually, I just tried the gmx
command to get autocorrelation. I did not know that xmgrace can perform
that. I will try to get ACF with xmgrace and then compare the results.

Regards,
Farideh

On Mon, Jan 23, 2017 at 6:55 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> I can reproduce your result, and if I change the value of a single
> datapoint by, say 5% or so, I get a non-zero acf. It could be that cmx
> analyze is too insensitive for numeric reasons, or it could also be that
> your data is too sparsely sampled to contain any trace of “memory” in the
> system. Have you tried calculating the act by other means, xmgrace for
> instance? Does that yield a similar result?
>
> Kind regards,
> Erik
>
> > On 23 Jan 2017, at 12:08, faride badalkhani <farideh.khamseh at gmail.com>
> wrote:
> >
> > Kindly find the Rg plot in the following link:
> >
> > https://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLigand.xlsx?dl=0
> >
> > Let me know if you need any other files or information.
> >
> > Regards,
> > F.
> >
> > On Mon, Jan 23, 2017 at 2:07 PM, Erik Marklund <erik.marklund at kemi.uu.se
> >
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks. And the file Rg.xvg looks sound?
> >>
> >> Kind regards,
> >> Erik
> >>
> >>> On 23 Jan 2017, at 11:33, faride badalkhani <farideh.khamseh at gmail.com
> >
> >> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Thanks for the answer. I used the autocorrelation function of the
> squared
> >>> radius of gyration cross-correlation of time course of Rg with itself
> >> with
> >>> the following command
> >>> gmx analyze -f Rg.xvg -ac
> >>>
> >>> and the autocorrelation is exactly zero.
> >>>
> >>> it is worth mentioning that I have performed the same PMF calculations
> >> on a
> >>> polymer-drug system and I did not have any problem in that case. The
> only
> >>> difference of that system with this one was in the terminal groups of
> >>> polymer. The first polymer has protonated surface groups (NH3+) but the
> >>> second one is neutral (acetylene).
> >>>
> >>> Best,
> >>> F.
> >>>
> >>> On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <
> erik.marklund at kemi.uu.se
> >>>
> >>> wrote:
> >>>
> >>>> Dear Farideh,
> >>>>
> >>>> Can you please inform us about how you calculated the ac? Hard to help
> >>>> otherwise. Also, is it exactly zero or just very small numbers?
> >>>>
> >>>> Kind regards,
> >>>> Erik
> >>>>
> >>>>> On 23 Jan 2017, at 10:50, faride badalkhani <
> farideh.khamseh at gmail.com
> >>>
> >>>> wrote:
> >>>>>
> >>>>> Dear GROMACS users,
> >>>>>
> >>>>> I am performing umbrella sampling on a polymer-ligand system and I
> >>>> generate
> >>>>> configurations successfully but the problem is that when I plot the
> >>>>> autocorrelation function of Rg for each window it is zero for the
> whole
> >>>>> time of simulation. I changed the run time for each window but
> nothing
> >>>>> changed. Moreover, the initial polymer-ligand structure is
> equilibrated
> >>>>> well.
> >>>>> Any comment or suggestion will be greatly appreciated.
> >>>>>
> >>>>> Best,
> >>>>> Farideh
> >>>>> --
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